Genomics of Pear and Other Rosaceae Fruit Trees
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Breeding Science 66: 148–159 (2016) doi:10.1270/jsbbs.66.148 Review Genomics of pear and other Rosaceae fruit trees Toshiya Yamamoto* and Shingo Terakami NARO Institute of Fruit Tree Science, 21 Fujimoto, Tsukuba, Ibaraki 3058605, Japan The family Rosaceae includes many economically important fruit trees, such as pear, apple, peach, cherry, quince, apricot, plum, raspberry, and loquat. Over the past few years, wholegenome sequences have been released for Chinese pear, European pear, apple, peach, Japanese apricot, and strawberry. These sequences help us to conduct functional and comparative genomics studies and to develop new cultivars with desirable traits by marker-assisted selection in breeding programs. These genomics resources also allow identification of evolutionary relationships in Rosaceae, development of genomewide SNP and SSR markers, and construction of reference genetic linkage maps, which are available through the Genome Database for the Rosaceae web site. Here, we review the recent advances in genomics studies and their practical applications for Rosaceae fruit trees, particularly pear, apple, peach, and cherry. Key Words: apple, colinearity, genome sequence, peach, pear, reference map. Introduction al. 1996). Loquat (Eriobotrya japonica (Thunb.) Lindl.) is also an important fruit tree that belongs to the tribe Pyreae The family Rosaceae consists of about 2500 species from along with pears and apples. Several Prunus (“stone fruit”) 90 genera and includes diverse plants, which are primarily species are also important fruit trees and include peaches native to temperate regions (Hummer and Janick 2009). and nectarines (P. persica (L.) Batsch), plums (P. domestica This family was traditionally classified into several subfam L., P. salicina Lindl.), apricots (P. armeniaca L., P. mume ilies: Amygdaloideae, Maloideae, Rosoideae, Spiraeoideae, Siebold et Zucc.), and cherries (P. avium L., P. cerasus L.), and others (Hummer and Janick 2009). In 2007, three sub which belong to the subfamily Amygdaloideae, tribe families were suggested: Dryadoideae, Rosoideae and Amygdaleae. Annual world fruit production (in million Amygdaloideae (Potter et al. 2007); the latter subfamily tons) is as follows: peaches and nectarines, 21.6; plums, includes the former Amygdaloideae, Maloideae and 11.5; apricots, 4.1; and cherries 2.3 (FAOSTAT 2013). In Spiraeoideae. Many economically important crops produc Japan, domestic fruit production (in thousand tons) is as ing edible fruits (e.g., apple, apricot, cherry, loquat, peach, follows: apples, 742; pears, 294; peaches, 125; apricots, pear, plum, quince, raspberry, and strawberry), nuts (e.g., al 124; plums, 21; and cherries, 18 (FAOSTAT 2013). mond), and ornamentals (e.g., rose) belong to the Rosaceae. Basic chromosome number x = 7, 8, 9, 15 or 17 was ob The most economically important members of the served for Rosaceae members (Dirlewanger et al. 2009b, Rosaceae are apples (Malus × domestica Borkh.) and pears Evans and Campbell 2002, Potter et al. 2007). The subfami (Pyrus spp.), both of which belong to the subfamily ly Rosoideae, which contains rose, raspberry, and straw Amygdaloideae, tribe Pyreae. Annual world fruit production berry, has x = 7. The tribe Amygdaleae of subfamily of apples exceeds 80 million tons (FAOSTAT 2013), making Amygdaloideae, known for almond, apricot, cherry, peach, them the third most important fruit (after citrus and banana). and plum, has x = 8. The former subfamily Spiraeoideae Pears are the second most important fruit species in Rosaceae, (tribe Spiraeeae of subfamily Amygdaloideae,) has x = 9. with world production of approximately 25.2 million tons Basic chromosome number x = 17 is observed for the tribe (FAOSTAT 2013). Four important Pyrus species are com Pyreae of subfamily Amygdaloideae, which contains apple, mercially grown for edible fruit: Japanese pear (P. pyrifolia loquat, pear, and quince. Challice (1974, 1981) suggested Nakai), European pear (P. communis L.), and Chinese pears that the Pyreae was generated by an allopolyploidization (P. bretschneideri Rehd. and P. ussuriensis Maxim.) (Bell et event between “Amygdaleae” (x = 8) and “Spiraeeae” (x = 9). Recent molecular genetic studies contradicted the Communicated by M. Omura allopolyploidization and supported the autopolyploid origin Received September 10, 2015. Accepted January 12, 2016. of hybridization between closely related members of *Corresponding author (email: [email protected]) Spiraeeae (Evans and Campbell 2002). Velasco et al. (2010) 148 Breeding Science Genomics of pear and other Rosaceae fruit trees Vol. 66 No. 1 BS showed that a relatively recent (ca. 50 million years ago) and covers a total of 577.3 Mb (96.2% of the estimated genomewide duplication resulted in the transition from genome size, 600 Mb). A total of 43,419 putative genes nine ancestral chromosomes to 17 chromosomes in apple, were predicted, of which 1219 are unique to European pear based on wholegenome sequencing analysis. and are not found in other dicots plant genomes sequenced. In recent years, international collaborative studies by the Analysis of the expansin gene family and other cell wall Rosaceae research community have hastened progress in related genes showed their involvement in fruit softening developing genetic and genomic resources for representa in both European pear and apple. It is expected that pear tive crops such as apple (M. × domestica), peach (P. persica), genome sequences of Chinese and European pears will be and strawberry (Fragaria spp.) (Shulaev et al. 2008); this assigned to 17 pseudochromosomes, which will greatly strategy was based on a consensus that there are multiple help us to conduct genetics and genomics studies in pears. Rosaceae model species (Dirlewanger et al. 2009b). These An international consortium has published a draft ge resources, including expressed sequence tags (ESTs), bac nome sequence of the domesticated apple ‘Golden terial artificial chromosome (BAC) libraries, physical and Delicious’, a common founder cultivar in many breeding genetic maps, and molecular markers and bioinformatics programs (Velasco et al. 2010). The genome assembly of tools, are available through the Genome Database for the ‘Golden Delicious’ consists of 122,146 contigs spanning a Rosaceae (GDR; http://www.rosaceae.org). The availability total of 603.9 Mb (81.3% of the estimated genome, of this database has rendered various rosaceous crops highly 742.3 Mb). Seventeen pseudochromosomes (GDR, Malus amenable to functional and comparative genomics studies. × domestica Genome v1.0p) were obtained from these con Here we review recent progress in genomics studies on tigs. A total of 57,386 putative proteincoding genes were Rosaceae fruit trees such as apple, pear, peach, and cherry, predicted. The MADS-box gene family involved in flower and we discuss the newly accumulated knowledge and re and fruit development is expanded in apple to 15 members. sources for comparative genomics studies on this family. The other gene families related with transport and assimila tion of sorbitol are also expanded, and are involved in Genome sequences of Rosaceae fruit crops Rosaceae-specific metabolism. A highquality draft reference genome sequence, Peach Wholegenome sequences have been reported for Chinese v1.0, of the doubled haploid genotype of the peach cultivar pear (Wu et al. 2013), European pear (Chagné et al. 2014), ‘Lovell’ has been reported (Verde et al. 2013). Since apple (Velasco et al. 2010), peach (Verde et al. 2013), Japa ‘Lovell’ is completely homozygous, its genome assembly nese apricot (Zhang et al. 2012), wild strawberry (Shulaev has facilitated obtaining a reliable and unbiased reference et al. 2011) and cultivated strawberry (Hirakawa et al. genome. Using 827 markers from an updated Prunus ref 2014) (Table 1). The draft genome of the Chinese pear erence map (Howad et al. 2005), Verde et al. (2013) or ‘Dangshansuli’ (P. bretschneideri) is now available (Wu et ganized 215.9 Mb of the Peach v1.0 genome into eight al. 2013). A total of 2103 scaffolds span 512.0 Mb (97.1% pseudomolecules covering 81.5% of the estimated genome of the estimated genome size, 527 Mb) and are not anchored (265 Mb). A total of 27,852 proteincoding genes were pre to the 17 chromosomes. The Chinese pear genome assembly dicted. Furthermore, comparative analyses showed that the contains 42,812 proteincoding genes, and about 28.5% of ancestral triplicated blocks in peach are detected, and that them encode multiple isoforms. The identified repetitive se putative paleoancestor regions are detectable. quences (271.9 Mb in total) account for 53.1% of the ge The genome of Japanese apricot or mei (P. mume) was nome. The difference in size between the pear and apple one of the first genomes to be sequenced in the subgenus genomes is mainly due to the presence of repetitive se Prunus of the genus Prunus (Zhang et al. 2012). Japanese quences (predominantly transposable elements), whereas apricot was domesticated in China more than 3000 years genic regions and proteincoding genes are similar in both ago as an ornamental plant and fruit tree. A 237Mb genome species. A draft genome assembly of European pear assembly was generated from 29,989 scaffolds, 84.6% of ‘Bartlett’ (Chagné et al. 2014) contains 142,083 scaffolds which were further anchored to eight chromosomes in a Table 1. Details of wholegenome sequencing in Rosaceae crops Pyrus bretschneideri Pyrus communis Malus × domestica Prunus persica Prunus mume Fragaria vesca Common name Chinese pear European pear apple peach Japanese apricot woodland strawberry Cultivar name Dangshansuli Bartlett Golden Delicious Lovell BJFU1210120008 Hawaii 4 (PI551572) No. of contigs 25,312 182,196 122,146 – 45,592 – No. of scaffolds 2103 142,083 – 391 29,989 3263 Genome assembly size (Mb) 512.0 577.3 603.9 215.9 237 209.8 Coverage (%) 97.1 96.2 81.3 81.5 84.6 95 Estimated genome size (Mb) 527 600 742.3 265 280 240 No. of putative genes 42,812 43,419 57,386 27,852 31,390 34,809 No. of pseudochromosomes – – 17 8 8 7 Reference Wu et al.